Analysis of multiple analytes in archival dried blood spots obtained from newborn infants is a valuable tool for assessing a number of biological events (inflammation, immune dysfunction, coagulation abnormalities) present at birth. A recycling immunoaffinity chromatographic (RIC) system has been developed for isolating and measuring up to 52 different analytes in approximately one third of a heel stab blood spot dried on chromatography filter paper. This system allows investigators to examine and compare a number of important biological systems within the same sample. Applied to samples obtained from children with clinical diagnoses of cerebral palsy and autism, distinct patterns are beginning to emerge. In cerebral palsy, elevations of certain cytokines demonstrated a correlation with the clinical status of the patient while in autism certain neuropeptides demonstrated a similar trend. These studies are being extended to examination of other cohorts of archival materials and to extending the array of detectable analytes. Additionally, studies are being performed using mass spectrometry to determine the physico-chemical characteristics of the molecules measured and evaluating their potential as clinical biomarkers.